Pan Du

Summary

Affiliation: Northwestern University
Country: USA

Publications

  1. ncbi request reprint 2009 and beyond: the decade of personalised medicine
    Pan Du
    The Biomedical Informatics Center, Northwestern University, Chicago, IL 60611, USA
    Int J Comput Biol Drug Des 1:329-33. 2008
  2. doi request reprint lumi: a pipeline for processing Illumina microarray
    Pan Du
    Robert H Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
    Bioinformatics 24:1547-8. 2008
  3. pmc Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis
    Pan Du
    Northwestern University Biomedical Informatics Center NUBIC, NUCATS, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
    BMC Bioinformatics 11:587. 2010
  4. pmc Gene expression and functional studies of the optic nerve head astrocyte transcriptome from normal African Americans and Caucasian Americans donors
    Haixi Miao
    Department of Ophthalmology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
    PLoS ONE 3:e2847. 2008
  5. pmc L-methionine-induced alterations in molecular signatures in MCF-7 and LNCaP cancer cells
    Maximo A Benavides
    Department of Pathology, College of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
    J Cancer Res Clin Oncol 137:441-53. 2011
  6. pmc Gene expression variation between African Americans and whites is associated with coronary artery calcification: the multiethnic study of atherosclerosis
    Chiang Ching Huang
    Department of Preventive Medicine, Northwestern University, Chicago, Illinois, USA
    Physiol Genomics 43:836-43. 2011
  7. pmc Genome-wide study of DNA methylation alterations in response to diazinon exposure in vitro
    Xiao Zhang
    Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
    Environ Toxicol Pharmacol 34:959-68. 2012
  8. pmc DNA methylation alterations in response to pesticide exposure in vitro
    Xiao Zhang
    Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
    Environ Mol Mutagen 53:542-9. 2012
  9. pmc Visual presentation as a welcome alternative to textual presentation of gene annotation information
    Jairav Desai
    The Biomedical Informatics Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
    Adv Exp Med Biol 680:709-15. 2010
  10. pmc Egr-1 induces a profibrotic injury/repair gene program associated with systemic sclerosis
    Swati Bhattacharyya
    Division of Rheumatology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
    PLoS ONE 6:e23082. 2011

Collaborators

Detail Information

Publications26

  1. ncbi request reprint 2009 and beyond: the decade of personalised medicine
    Pan Du
    The Biomedical Informatics Center, Northwestern University, Chicago, IL 60611, USA
    Int J Comput Biol Drug Des 1:329-33. 2008
    ....
  2. doi request reprint lumi: a pipeline for processing Illumina microarray
    Pan Du
    Robert H Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
    Bioinformatics 24:1547-8. 2008
    ..Availability: The lumi Bioconductor package, www.bioconductor.org..
  3. pmc Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis
    Pan Du
    Northwestern University Biomedical Informatics Center NUBIC, NUCATS, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
    BMC Bioinformatics 11:587. 2010
    ..Both Beta-value and M-value statistics have been used as metrics to measure methylation levels. However, there are no detailed studies of their relations and their strengths and limitations...
  4. pmc Gene expression and functional studies of the optic nerve head astrocyte transcriptome from normal African Americans and Caucasian Americans donors
    Haixi Miao
    Department of Ophthalmology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
    PLoS ONE 3:e2847. 2008
    ....
  5. pmc L-methionine-induced alterations in molecular signatures in MCF-7 and LNCaP cancer cells
    Maximo A Benavides
    Department of Pathology, College of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
    J Cancer Res Clin Oncol 137:441-53. 2011
    ..Methionine inhibits proliferation of breast and prostate cancer cells. Here, we determined the influence of L-methionine on functional molecular signatures in these cell lines...
  6. pmc Gene expression variation between African Americans and whites is associated with coronary artery calcification: the multiethnic study of atherosclerosis
    Chiang Ching Huang
    Department of Preventive Medicine, Northwestern University, Chicago, Illinois, USA
    Physiol Genomics 43:836-43. 2011
    ..Our data suggest a connection between immune response and vascular calcification and the result provides a potential mechanistic explanation for the lower prevalence and severity of CAC in African Americans compared with whites...
  7. pmc Genome-wide study of DNA methylation alterations in response to diazinon exposure in vitro
    Xiao Zhang
    Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
    Environ Toxicol Pharmacol 34:959-68. 2012
    ..2-fold, q-value=0.002), and some remain functionally unknown. Our results provided direct experimental evidence that diazinon may modify gene promoter DNA methylation levels, which may play a pathological role in cancer development...
  8. pmc DNA methylation alterations in response to pesticide exposure in vitro
    Xiao Zhang
    Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
    Environ Mol Mutagen 53:542-9. 2012
    ..Further studies in other cell types and human samples are required, as well as determining the impact of these methylation changes on gene expression...
  9. pmc Visual presentation as a welcome alternative to textual presentation of gene annotation information
    Jairav Desai
    The Biomedical Informatics Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
    Adv Exp Med Biol 680:709-15. 2010
    ..Moreover, the survey participants provided many constructive comments that will specify the development of a phase-two project (http://128.248.174.241/) to visually annotate each gene in the human genome...
  10. pmc Egr-1 induces a profibrotic injury/repair gene program associated with systemic sclerosis
    Swati Bhattacharyya
    Division of Rheumatology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
    PLoS ONE 6:e23082. 2011
    ..These observations suggest that targeting Egr-1 expression or activity might be a novel therapeutic strategy to control fibrosis in specific SSc subsets...
  11. doi request reprint Gene expression changes in retinal Müller (glial) cells exposed to elevated pressure
    Wei Xue
    Department of Ophthalmology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 606111, USA
    Curr Eye Res 36:754-67. 2011
    ..To address this question, we have examined gene expression changes in Müller cells exposed to elevated pressure...
  12. pmc Genome-wide DNA methylation indicates silencing of tumor suppressor genes in uterine leiomyoma
    Antonia Navarro
    Division of Reproductive Biology Research, Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
    PLoS ONE 7:e33284. 2012
    ..Epigenetic dysregulation of individual genes has been demonstrated in leiomyoma cells; however, the in vivo genome-wide distribution of such epigenetic abnormalities remains unknown...
  13. pmc Model-based variance-stabilizing transformation for Illumina microarray data
    Simon M Lin
    Robert H Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, 60611, USA
    Nucleic Acids Res 36:e11. 2008
    ..The algorithms and Supplementary Data are included in the lumi package of Bioconductor, available at: www.bioconductor.org...
  14. pmc The early growth response gene Egr2 (Alias Krox20) is a novel transcriptional target of transforming growth factor-β that is up-regulated in systemic sclerosis and mediates profibrotic responses
    Feng Fang
    Division of Rheumatology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
    Am J Pathol 178:2077-90. 2011
    ..Together, these findings suggest that Egr-2 plays an important nonredundant role in the pathogenesis of fibrosis. Targeting Egr-2 might represent a novel therapeutic strategy to control fibrosis...
  15. ncbi request reprint Suppression by L-methionine of cell cycle progression in LNCaP and MCF-7 cells but not benign cells
    Maximo A Benavides
    Department of Pathology, University of Illinois at Chicago, College of Medicine, 840 South Wood Street, Chicago, Illinois 60612, USA
    Anticancer Res 30:1881-5. 2010
    ..Methionine inhibits proliferation of breast and prostate cancer cells. This study aimed to determine cell cycle effects of methionine and selectivity for cancer cells...
  16. pmc Activated TLR signaling in atherosclerosis among women with lower Framingham risk score: the multi-ethnic study of atherosclerosis
    Chiang Ching Huang
    Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
    PLoS ONE 6:e21067. 2011
    ....
  17. doi request reprint Genomics of human intracranial aneurysm wall
    Changbin Shi
    Department of Neurological Surgery, Center for Genetic Medicine, and Robert H Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Ill 60611, USA
    Stroke 40:1252-61. 2009
    ..However, a broad view of pathologic mechanisms has not been investigated by identifying pathogenic genes and their interaction in networks. Our study aimed to analyze global gene expression patterns in the IA wall...
  18. pmc From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose ontology for the test of gene-ontology associations
    Pan Du
    The Biomedical Informatics Center, Northwestern University, Chicago, IL 60611, USA
    Bioinformatics 25:i63-8. 2009
    ..The resultant DOLite has been used in the Functional Disease Ontology (FunDO) Web application at http://www.projects.bioinformatics.northwestern.edu/fundo...
  19. ncbi request reprint A divide-and-conquer strategy to solve the out-of-memory problem of processing thousands of Affymetrix microarrays
    Chia Ju Lee
    Computational Biology and Bioinformatics Program, Northwestemrn University, Evanston, IL 60208, USA
    Int J Comput Biol Drug Des 1:396-405. 2008
    ..In addition to the performance improvement, the general divide-and-conquer strategy can be applied to any other normalisation algorithms without modifying the underlying implementation...
  20. pmc A collection of bioconductor methods to visualize gene-list annotations
    Gang Feng
    Northwestern University Biomedical Informatics Center NUBIC, part of the Northwestern CTSA and The Robert H, Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
    BMC Res Notes 3:10. 2010
    ..abstract:..
  21. pmc Susceptibility to glaucoma: differential comparison of the astrocyte transcriptome from glaucomatous African American and Caucasian American donors
    Thomas J Lukas
    Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, E Chicago Ave, Chicago, IL 60611, USA
    Genome Biol 9:R111. 2008
    ....
  22. pmc Epithelial regulation of mesenchymal tissue behavior
    Corrie L Gallant-Behm
    Department of Surgery, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
    J Invest Dermatol 131:892-9. 2011
    ..These results support the idea that soluble factors produced by the epithelium in response to injury may influence fibroblast behavior and regulate scar formation in vivo...
  23. ncbi request reprint Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching
    Pan Du
    Robert H Lurie Comprehensive Cancer Center, Northwestern University Chicago, IL 60611, USA
    Bioinformatics 22:2059-65. 2006
    ..This approach is very sensitive to the amount of smoothing and aggressiveness of the baseline correction, which contribute to making peak detection results inconsistent between runs, instrumentation and analysis methods...
  24. pmc Expression of cyclophilin B is associated with malignant progression and regulation of genes implicated in the pathogenesis of breast cancer
    Feng Fang
    Breast Cancer Program, Robert H Lurie Comprehensive Cancer Center and Department of Pathology, Northwestern University, Chicago, Illinois 60611, USA
    Am J Pathol 174:297-308. 2009
    ....
  25. pmc Using Free and Open-Source Bioconductor Packages to Analyze Array Comparative Genomics Hybridization (aCGH) Data
    Simon Lin
    Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
    Curr Genomics 10:60-3. 2009
    ..We review several free and open-source packages in Bioconductor and provide example codes to run the analysis. The analysis of aCGH data provides insights of genomic abnormalities of cancers...
  26. ncbi request reprint Modeling gene expression networks using fuzzy logic
    Pan Du
    Virtual Reality Applications Center, Iowa State University, Ames 50011 3060, USA
    IEEE Trans Syst Man Cybern B Cybern 35:1351-9. 2005
    ..Key gene regulatory relationships were evaluated using information from the gene ontology database. A new regulatory relationship concerning trehalose regulation of carbohydrate metabolism was also discovered in the extracted network...